Analysis of genetic effects on disease conferred by clusters of related and highly polymorphic genes poses substantial problems in terms of the identification of the true disease locus once an association has been observed. Understanding and accounting for the molecular genetic properties that operate over the locus is essential for accurate interpretation of both disease association data and analysis of functional interactions between the molecules encoded in the major histocompatibility complex (MHC). Completion of the entire sequencing of the MHC has provided us with an invaluable tool for defining some of these properties.[unreadable] [unreadable] Comparing patterns of linkage disequilibrium (LD) between pairs of markers with recombination fractions for the segment separating those pairs of loci can provide information regarding selective pressure to maintain linkage of specific combinations of alleles. We have previously shown that a region in human leukocyte antigen (HLA) class III located between the BAT2 and LTA genes (45 kb), which was characterized as the strongest hot spot within the MHC, actually exhibited significant variation in recombination rate across twelve individual sperm donors. We hypothesized that level of the sequence similarity between homologous chromosomes of a given individual in a particular chromosomal segment and rate of recombination would be correlated positively. Thus, in collaboration with th Sanger Centre at Cambridge University, we have nearly completed sequence analysis of this 45 kb fragment in 6 individuals whose recombination rates vary significantly in this area. The region was amplified in 12 overlapping 5-6 kb segments and mini-libraries were generated corresponding to each 5-6Kb amplicon. Complete sequences of the 45 kb fragment will be assembled by our laboratory with the assistance of the ABCC, and level of sequence similarity will be analyzed in each individual to determine if there is a correlation with recombination rate. Through the International Histocompatibility Workshops, HLA allelic distributions across populations have been investigated. This organized transcontinental cooperation among HLA typing labs provides a unique and invaluable resource of HLA data that may not otherwise be available to the community. Historically, however, the data have suffered limitations in terms of typing resolution, consistency in typing protocols across laboratories, and numbers of samples typed for some populations. We have had the fortunate opportunity to genotype both the HLA class I and killer immunoglobulin-like receptor (KIR) loci in sets of samples (ranging in size from 23-129 individuals) from 29 worldwide populations. KIR and HLA typing have been completed on the majority of the 1612 samples sent to us and we will soon begin the process of analyzing the data. We have also received 320 DNA samples representing distinct tribes from rural southern Cameroon that will be included in our population analysis of these genes. Consideration of these data in terms of physical world map location of the various populations may provide clues to potential selection processes that have occurred differentially across the populations.